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Yorodumi- PDB-5yql: Crystal structure of Sirt2 in complex with selective inhibitor A2I -
+Open data
-Basic information
Entry | Database: PDB / ID: 5yql | ||||||
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Title | Crystal structure of Sirt2 in complex with selective inhibitor A2I | ||||||
Components | NAD-dependent protein deacetylase sirtuin-2 | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / NAD-dependent deacetylase sirtuin-2 / Inhibitor / Complex / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information cellular response to caloric restriction / negative regulation of oligodendrocyte progenitor proliferation / : / negative regulation of striated muscle tissue development / negative regulation of satellite cell differentiation / histone H4K16 deacetylase activity, NAD-dependent / positive regulation of attachment of spindle microtubules to kinetochore / positive regulation of meiotic nuclear division / NAD-dependent protein demyristoylase activity / NAD-dependent protein depalmitoylase activity ...cellular response to caloric restriction / negative regulation of oligodendrocyte progenitor proliferation / : / negative regulation of striated muscle tissue development / negative regulation of satellite cell differentiation / histone H4K16 deacetylase activity, NAD-dependent / positive regulation of attachment of spindle microtubules to kinetochore / positive regulation of meiotic nuclear division / NAD-dependent protein demyristoylase activity / NAD-dependent protein depalmitoylase activity / tubulin deacetylation / paranodal junction / lateral loop / NLRP3 inflammasome complex assembly / peptidyl-lysine deacetylation / negative regulation of NLRP3 inflammasome complex assembly / mitotic nuclear membrane reassembly / tubulin deacetylase activity / regulation of exit from mitosis / paranode region of axon / Schmidt-Lanterman incisure / NAD-dependent protein lysine deacetylase activity / positive regulation of fatty acid biosynthetic process / myelination in peripheral nervous system / rDNA heterochromatin formation / protein acetyllysine N-acetyltransferase / histone deacetylase activity, NAD-dependent / chromatin silencing complex / Initiation of Nuclear Envelope (NE) Reformation / protein deacetylation / regulation of phosphorylation / positive regulation of oocyte maturation / juxtaparanode region of axon / protein lysine deacetylase activity / meiotic spindle / response to redox state / regulation of myelination / histone deacetylase activity / histone acetyltransferase binding / positive regulation of DNA binding / negative regulation of fat cell differentiation / negative regulation of peptidyl-threonine phosphorylation / positive regulation of execution phase of apoptosis / positive regulation of cell division / glial cell projection / NAD+-protein poly-ADP-ribosyltransferase activity / NAD+ binding / subtelomeric heterochromatin formation / negative regulation of reactive oxygen species metabolic process / heterochromatin / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / cellular response to epinephrine stimulus / substantia nigra development / centriole / epigenetic regulation of gene expression / negative regulation of autophagy / ubiquitin binding / meiotic cell cycle / negative regulation of protein catabolic process / heterochromatin formation / mitotic spindle / histone deacetylase binding / spindle / autophagy / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / myelin sheath / chromosome / cellular response to oxidative stress / cellular response to hypoxia / midbody / growth cone / perikaryon / proteasome-mediated ubiquitin-dependent protein catabolic process / DNA-binding transcription factor binding / microtubule / chromosome, telomeric region / regulation of cell cycle / cell division / innate immune response / negative regulation of DNA-templated transcription / centrosome / chromatin binding / nucleolus / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion / zinc ion binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.601 Å | ||||||
Authors | Wang, H. / Yu, Y. / Li, G. / Chen, Q. | ||||||
Citation | Journal: Eur J Med Chem / Year: 2018 Title: X-ray crystal structure guided discovery of new selective, substrate-mimicking sirtuin 2 inhibitors that exhibit activities against non-small cell lung cancer cells. Authors: Yang, L.L. / Wang, H.L. / Zhong, L. / Yuan, C. / Liu, S.Y. / Yu, Z.J. / Liu, S. / Yan, Y.H. / Wu, C. / Wang, Y. / Wang, Z. / Yu, Y. / Chen, Q. / Li, G.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5yql.cif.gz | 132.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yql.ent.gz | 100.9 KB | Display | PDB format |
PDBx/mmJSON format | 5yql.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5yql_validation.pdf.gz | 732.3 KB | Display | wwPDB validaton report |
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Full document | 5yql_full_validation.pdf.gz | 733.1 KB | Display | |
Data in XML | 5yql_validation.xml.gz | 17 KB | Display | |
Data in CIF | 5yql_validation.cif.gz | 26.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yq/5yql ftp://data.pdbj.org/pub/pdb/validation_reports/yq/5yql | HTTPS FTP |
-Related structure data
Related structure data | 5yqmC 5yqnC 5yqoC 5matS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 34449.668 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SIRT2, SIR2L, SIR2L2 / Production host: Escherichia coli (E. coli) References: UniProt: Q8IXJ6, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides | ||
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#2: Chemical | ChemComp-A2I / | ||
#3: Chemical | ChemComp-ZN / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.78 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.2M Magnesium Formate, 23-30% (v/v) Polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 24, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 37723 / % possible obs: 98.2 % / Redundancy: 3.3 % / Rpim(I) all: 0.07 / Net I/σ(I): 10 |
Reflection shell | Highest resolution: 1.6 Å / CC1/2: 0.791 / Rpim(I) all: 0.276 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5MAT Resolution: 1.601→35.895 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.46
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.601→35.895 Å
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Refine LS restraints |
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LS refinement shell |
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